Hi Gianmarco, you can add hydrogens with coordinates keeping the current heavy atom coordinates with
rdkit_mol = rdkit.Chem.AddHs(rdkit_mol, addCoords=True) so you may avoid having to call EmbedMolecule, which will compute a whole set of new coordinates for your molecule. I hope I interpreted your needs correctly! Cheers, p. On Thu, Jan 13, 2022 at 2:05 PM Gianmarco Ghiandoni <ghiandon...@gmail.com> wrote: > Hi all, > > Quick question: I have noticed that when I read a compound from an SDF/Mol > file where all coordinates are already defined, the embedding process > changes the conformation of the RDKit mol object, hence coordinates are not > preserved: > > import rdkit > cdk2_path = os.path.join(data_path, "cdk2_validation") > rdkit_mol = rdkit.Chem.MolFromMolFile(os.path.join(cdk2_path, "26Z.sdf")) > rdkit_mol = rdkit.Chem.AddHs(rdkit_mol) > rdkit.Chem.AllChem.EmbedMolecule(rdkit_mol) > > What is the best practice for reading a molecule with coordinates without > shuffling them? (e.g. for a ligand from the PDB). > > Thanks, > -- > *Gianmarco* > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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